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mutate.py
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mutate.py
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'''
Written by Jan H. Jensen 2018
'''
from rdkit import Chem
from rdkit.Chem import AllChem
import random
import numpy as np
import crossover as co
#from io import StringIO
#import sys
#sio = sys.stderr = StringIO()
from rdkit import rdBase
rdBase.DisableLog('rdApp.error')
def delete_atom():
choices = ['[*:1]~[D1:2]>>[*:1]', '[*:1]~[D2:2]~[*:3]>>[*:1]-[*:3]',
'[*:1]~[D3:2](~[*;!H0:3])~[*:4]>>[*:1]-[*:3]-[*:4]',
'[*:1]~[D4:2](~[*;!H0:3])(~[*;!H0:4])~[*:5]>>[*:1]-[*:3]-[*:4]-[*:5]',
'[*:1]~[D4:2](~[*;!H0;!H1:3])(~[*:4])~[*:5]>>[*:1]-[*:3](-[*:4])-[*:5]']
p = [0.25,0.25,0.25,0.1875,0.0625]
return np.random.choice(choices, p=p)
def append_atom():
choices = [['single',['C','N','O','F','S','Cl','Br'],7*[1.0/7.0]],
['double',['C','N','O'],3*[1.0/3.0]],
['triple',['C','N'],2*[1.0/2.0]] ]
p_BO = [0.60,0.35,0.05]
index = np.random.choice(list(range(3)), p=p_BO)
BO, atom_list, p = choices[index]
new_atom = np.random.choice(atom_list, p=p)
if BO == 'single':
rxn_smarts = '[*;!H0:1]>>[*:1]X'.replace('X','-'+new_atom)
if BO == 'double':
rxn_smarts = '[*;!H0;!H1:1]>>[*:1]X'.replace('X','='+new_atom)
if BO == 'triple':
rxn_smarts = '[*;H3:1]>>[*:1]X'.replace('X','#'+new_atom)
return rxn_smarts
def insert_atom():
choices = [['single',['C','N','O','S'],4*[1.0/4.0]],
['double',['C','N'],2*[1.0/2.0]],
['triple',['C'],[1.0]] ]
p_BO = [0.60,0.35,0.05]
index = np.random.choice(list(range(3)), p=p_BO)
BO, atom_list, p = choices[index]
new_atom = np.random.choice(atom_list, p=p)
if BO == 'single':
rxn_smarts = '[*:1]~[*:2]>>[*:1]X[*:2]'.replace('X',new_atom)
if BO == 'double':
rxn_smarts = '[*;!H0:1]~[*:2]>>[*:1]=X-[*:2]'.replace('X',new_atom)
if BO == 'triple':
rxn_smarts = '[*;!R;!H1;!H0:1]~[*:2]>>[*:1]#X-[*:2]'.replace('X',new_atom)
return rxn_smarts
def change_bond_order():
choices = ['[*:1]!-[*:2]>>[*:1]-[*:2]','[*;!H0:1]-[*;!H0:2]>>[*:1]=[*:2]',
'[*:1]#[*:2]>>[*:1]=[*:2]','[*;!R;!H1;!H0:1]~[*:2]>>[*:1]#[*:2]']
p = [0.45,0.45,0.05,0.05]
return np.random.choice(choices, p=p)
def delete_cyclic_bond():
return '[*:1]@[*:2]>>([*:1].[*:2])'
def add_ring():
choices = ['[*;!r;!H0:1]~[*;!r:2]~[*;!r;!H0:3]>>[*:1]1~[*:2]~[*:3]1',
'[*;!r;!H0:1]~[*!r:2]~[*!r:3]~[*;!r;!H0:4]>>[*:1]1~[*:2]~[*:3]~[*:4]1',
'[*;!r;!H0:1]~[*!r:2]~[*:3]~[*:4]~[*;!r;!H0:5]>>[*:1]1~[*:2]~[*:3]~[*:4]~[*:5]1',
'[*;!r;!H0:1]~[*!r:2]~[*:3]~[*:4]~[*!r:5]~[*;!r;!H0:6]>>[*:1]1~[*:2]~[*:3]~[*:4]~[*:5]~[*:6]1']
p = [0.05,0.05,0.45,0.45]
return np.random.choice(choices, p=p)
def change_atom(mol):
choices = ['#6','#7','#8','#9','#16','#17','#35']
p = [0.15,0.15,0.14,0.14,0.14,0.14,0.14]
X = np.random.choice(choices, p=p)
while not mol.HasSubstructMatch(Chem.MolFromSmarts('['+X+']')):
X = np.random.choice(choices, p=p)
Y = np.random.choice(choices, p=p)
while Y == X:
Y = np.random.choice(choices, p=p)
return '[X:1]>>[Y:1]'.replace('X',X).replace('Y',Y)
def mutate(mol,mutation_rate):
if random.random() > mutation_rate:
return mol
Chem.Kekulize(mol,clearAromaticFlags=True)
p = [0.15,0.14,0.14,0.14,0.14,0.14,0.15]
for i in range(10):
rxn_smarts_list = 7*['']
rxn_smarts_list[0] = insert_atom()
rxn_smarts_list[1] = change_bond_order()
rxn_smarts_list[2] = delete_cyclic_bond()
rxn_smarts_list[3] = add_ring()
rxn_smarts_list[4] = delete_atom()
rxn_smarts_list[5] = change_atom(mol)
rxn_smarts_list[6] = append_atom()
rxn_smarts = np.random.choice(rxn_smarts_list, p=p)
#print 'mutation',rxn_smarts
rxn = AllChem.ReactionFromSmarts(rxn_smarts)
new_mol_trial = rxn.RunReactants((mol,))
new_mols = []
for m in new_mol_trial:
m = m[0]
#print Chem.MolToSmiles(mol),mol_OK(mol)
if co.mol_OK(m) and co.ring_OK(m):
new_mols.append(m)
if len(new_mols) > 0:
return random.choice(new_mols)
return None
if __name__ == "__main__":
main()